Nope. FPSE incorporates itself through out the web account. You'll need to
stick with HTTP publishing aka Web Folders aka Network Places for your file
management. Actually once you start using Windows Explorer (my
recommendation) you'll find it so much easier. The forms will not work,
period, if you ftp publish. Any ftp connection puts FPSE at risk of
corruption. On that comment I'll mention that from my own experiences and
testing I have found that an ftp connection outside the root web is ok. For
example my web host has the web account on a www folder, that's the root, but
they have the traffic logs outside that in a logs folder. Which I can safely
ftp to and obtain the log files. With FPSE you can create subwebs (that's how
you password protect btw) and do some other things via the FPSE admin page.
To access that on your FPSE (2002 or 2003) equipped web just add the
following "after" your domain URL -

_vti_bin/_vti_adm/fpadmdll.dll